r1005 - in trunk: echobase-domain/src/main/java/fr/ifremer/echobase/csv echobase-domain/src/main/java/fr/ifremer/echobase/entities/references echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser echobase-ui/src/main/resources - Echobase-commits

5 Apr 2014

Author: tchemit
Date: 2014-04-05 18:58:54 +0200 (Sat, 05 Apr 2014)
New Revision: 1005

Url: http://forge.codelutin.com/projects/echobase/repository/revisions/1005

Log:
refs #4704 fix species code

Added:
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java
Modified:
   trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java
   trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/references/SpeciesImpl.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportModel.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportRow.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportRow.java
   trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportModel.java
   trunk/echobase-ui/src/main/resources/struts.xml

Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java
===================================================================

--- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/csv/EchoBaseCsvUtil.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -25,6 +25,8 @@
 import fr.ifremer.echobase.entities.data.Voyage;
 import fr.ifremer.echobase.entities.references.DataMetadata;
 import fr.ifremer.echobase.entities.references.DataQuality;
+import fr.ifremer.echobase.entities.references.Species;
+import org.nuiton.csv.ValueFormatter;
 import org.nuiton.csv.ValueParser;
 import org.nuiton.csv.ValueParserFormatter;
 import org.nuiton.csv.ValueSetter;
@@ -48,6 +50,12 @@
 
     public static final ValueParser<Date> IMPORT_DAY_TIME_ECHOBASE2 = new DateValue("dd/MM/yyyy HH:mm:ss.SSSS");
 
+    public static final ValueFormatter<Species> SPECIES_TO_COSER_CODE = new ValueFormatter<Species>() {
+        @Override
+        public String format(Species value) {
+            return value.getBaracoudaCode().replaceAll("_", "");
+        }
+    };
 
     public static final ValueParser<Boolean> INT_TO_BOOLEAN_PARSER = new ValueParser<Boolean>() {
 
@@ -124,9 +132,6 @@
 
     public static final String DEPTH_STRATUM_ID = "depthStratumId";
 
-    public static final ValueParserFormatter<Date> YEAR =
-            new DateValue("yyyy");
-
     protected EchoBaseCsvUtil() {
         // avoid instanciation on helper class
     }

Modified: trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/references/SpeciesImpl.java
===================================================================
--- trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/references/SpeciesImpl.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-domain/src/main/java/fr/ifremer/echobase/entities/references/SpeciesImpl.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -25,8 +25,4 @@
 
     private static final long serialVersionUID = 1L;
 
-    // used for coser species export
-    public String getTaxaCode() {
-        return "";
-    }
 }

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportModel.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -36,7 +36,7 @@
         super(separator);
         newColumnForExport("Campagne", EchoBaseCsvUtil.<CommunityIndicatorExportRow, String>newBeanProperty(CommunityIndicatorExportRow.PROPERTY_MISSION_NAME));
         newColumnForExport("Indicateur", EchoBaseCsvUtil.<CommunityIndicatorExportRow, String>newBeanProperty(CommunityIndicatorExportRow.PROPERTY_INDICATOR_NAME));
-        newColumnForExport("Espece", EchoBaseCsvUtil.<CommunityIndicatorExportRow, String>newBeanProperty(CommunityIndicatorExportRow.PROPERTY_SPECIES_NAME));
+        newColumnForExport("Espece", CommunityIndicatorExportRow.PROPERTY_SPECIES, EchoBaseCsvUtil.SPECIES_TO_COSER_CODE);
         newColumnForExport("Strate", CommunityIndicatorExportRow.PROPERTY_STRATUM);
         newColumnForExport("Annee", CommunityIndicatorExportRow.PROPERTY_DATE, EchoBaseCsvUtil.YEAR);
         newColumnForExport("Estimation", CommunityIndicatorExportRow.PROPERTY_ESTIMATION);

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/CommunityIndicatorExportRow.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -35,11 +35,11 @@
  */
 public class CommunityIndicatorExportRow {
 
-    public static final String PROPERTY_MISSION_NAME = "mission.name";
+    public static final String PROPERTY_MISSION_NAME = "mission." + Mission.PROPERTY_NAME;
 
-    public static final String PROPERTY_INDICATOR_NAME = "indicator.name";
+    public static final String PROPERTY_INDICATOR_NAME = "indicator." + DataMetadata.PROPERTY_NAME;
 
-    public static final String PROPERTY_SPECIES_NAME = "species.codeMemo";
+    public static final String PROPERTY_SPECIES = "species";
 
     public static final String PROPERTY_STRATUM = "stratum";
 

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/ExportCoserService.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -513,12 +513,17 @@
     //------------------------------------------------------------------------//
 
     protected void extractSpeciesFile(EchoBaseProject project) {
-        File speciesFile = project.getSpeciesDefinitionFile();
-        SpeciesExportModel speciesExportModel = new SpeciesExportModel(getCsvSeparator());
+        File file = project.getSpeciesDefinitionFile();
+        if (log.isInfoEnabled()) {
+            log.info("generate " + file);
+        }
+        SpeciesExportModel exportModel = new SpeciesExportModel(getCsvSeparator());
+        List<Species> speciesList = persistenceService.getSpecies();
+        List<SpeciesExportRow> rows = exportModel.toRows(speciesList);
         try {
-            Export.exportToFile(speciesExportModel, persistenceService.getSpecies(), speciesFile);
+            Export.exportToFile(exportModel, rows, file);
         } catch (Exception e) {
-            throw new EchoBaseTechnicalException("Could not export species list to " + speciesFile, e);
+            throw new EchoBaseTechnicalException("Could not export species list to " + file, e);
         }
     }
 }

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportModel.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -36,7 +36,7 @@
         super(separator);
         newColumnForExport("Campagne", EchoBaseCsvUtil.<PopulationIndicatorExportRow, String>newBeanProperty(PopulationIndicatorExportRow.PROPERTY_MISSION_NAME));
         newColumnForExport("Indicateur", EchoBaseCsvUtil.<PopulationIndicatorExportRow, String>newBeanProperty(PopulationIndicatorExportRow.PROPERTY_INDICATOR_NAME));
-        newColumnForExport("Espece", EchoBaseCsvUtil.<PopulationIndicatorExportRow, String>newBeanProperty(PopulationIndicatorExportRow.PROPERTY_SPECIES_NAME));
+        newColumnForExport("Espece", PopulationIndicatorExportRow.PROPERTY_SPECIES, EchoBaseCsvUtil.SPECIES_TO_COSER_CODE);
         newColumnForExport("Strate", PopulationIndicatorExportRow.PROPERTY_STRATUM);
         newColumnForExport("Annee", PopulationIndicatorExportRow.PROPERTY_DATE, EchoBaseCsvUtil.YEAR);
         newColumnForExport("Estimation", PopulationIndicatorExportRow.PROPERTY_ESTIMATION);

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/PopulationIndicatorExportRow.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -35,11 +35,11 @@
  */
 public class PopulationIndicatorExportRow {
 
-    public static final String PROPERTY_MISSION_NAME = "mission.name";
+    public static final String PROPERTY_MISSION_NAME = "mission." + Mission.PROPERTY_NAME;
 
-    public static final String PROPERTY_INDICATOR_NAME = "indicator.name";
+    public static final String PROPERTY_INDICATOR_NAME = "indicator." + DataMetadata.PROPERTY_NAME;
 
-    public static final String PROPERTY_SPECIES_NAME = "species.codeMemo";
+    public static final String PROPERTY_SPECIES = "species";
 
     public static final String PROPERTY_STRATUM = "stratum";
 

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportModel.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportModel.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportModel.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -83,7 +83,7 @@
         newColumnForExport("Campagne", EchoBaseCsvUtil.<RawDataCatchExportRow, String>newBeanProperty(RawDataCatchExportRow.PROPERTY_VOYAGE_NAME));
         newColumnForExport("Annee", EchoBaseCsvUtil.<RawDataCatchExportRow, Date>newBeanProperty(RawDataCatchExportRow.PROPERTY_VOYAGE_YEAR), EchoBaseCsvUtil.YEAR);
         newColumnForExport("Trait", EchoBaseCsvUtil.<RawDataCatchExportRow, String>newBeanProperty(RawDataCatchExportRow.PROPERTY_OPERATION_ID));
-        newColumnForExport("Espece", EchoBaseCsvUtil.<RawDataCatchExportRow, String>newBeanProperty(RawDataCatchExportRow.PROPERTY_SPECIES_CODE));
+        newColumnForExport("Espece", RawDataCatchExportRow.PROPERTY_SPECIES,EchoBaseCsvUtil.SPECIES_TO_COSER_CODE);
         newColumnForExport("Nombre", RawDataCatchExportRow.PROPERTY_OPERATION_NUMBER, EchoBaseCsvUtil.PRIMITIVE_INTEGER);
         newColumnForExport("Poids", RawDataCatchExportRow.PROPERTY_OPERATION_WEIGHT, EchoBaseCsvUtil.PRIMITIVE_FLOAT);
     }

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportRow.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportRow.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataCatchExportRow.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -33,15 +33,13 @@
  */
 public class RawDataCatchExportRow {
 
-    public static final String PROPERTY_VOYAGE = "voyage";
+    public static final String PROPERTY_SPECIES = "species";
 
-    public static final String PROPERTY_SPECIES_CODE = "species." + Species.PROPERTY_CODE_MEMO;
-
     public static final String PROPERTY_OPERATION_ID = "operation." + Operation.PROPERTY_ID;
 
-    public static final String PROPERTY_VOYAGE_NAME = PROPERTY_VOYAGE + "." + Voyage.PROPERTY_NAME;
+    public static final String PROPERTY_VOYAGE_NAME = "voyage." + Voyage.PROPERTY_NAME;
 
-    public static final String PROPERTY_VOYAGE_YEAR = PROPERTY_VOYAGE + "." + Voyage.PROPERTY_START_DATE;
+    public static final String PROPERTY_VOYAGE_YEAR = "voyage." + Voyage.PROPERTY_START_DATE;
 
     public static final String PROPERTY_OPERATION_NUMBER = "number";
 

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportModel.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -104,7 +104,7 @@
         newColumnForExport("Campagne", EchoBaseCsvUtil.<RawDataSizeExportRow, String>newBeanProperty(RawDataSizeExportRow.PROPERTY_VOYAGE_NAME));
         newColumnForExport("Annee", EchoBaseCsvUtil.<RawDataSizeExportRow, Date>newBeanProperty(RawDataSizeExportRow.PROPERTY_VOYAGE_YEAR), EchoBaseCsvUtil.YEAR);
         newColumnForExport("Trait", EchoBaseCsvUtil.<RawDataSizeExportRow, String>newBeanProperty(RawDataSizeExportRow.PROPERTY_OPERATION_ID));
-        newColumnForExport("Espece", EchoBaseCsvUtil.<RawDataSizeExportRow, String>newBeanProperty(RawDataSizeExportRow.PROPERTY_SPECIES_CODE));
+        newColumnForExport("Espece", RawDataSizeExportRow.PROPERTY_SPECIES, EchoBaseCsvUtil.SPECIES_TO_COSER_CODE);
         newColumnForExport("Sexe", RawDataSizeExportRow.PROPERTY_SEX_CATEGORY, new ValueFormatter<SexCategory>() {
             @Override
             public String format(SexCategory value) {

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportRow.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportRow.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/RawDataSizeExportRow.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -35,15 +35,13 @@
  */
 public class RawDataSizeExportRow {
 
-    public static final String PROPERTY_VOYAGE = "voyage";
+    public static final String PROPERTY_SPECIES = "species";
 
-    public static final String PROPERTY_SPECIES_CODE = "species." + Species.PROPERTY_CODE_MEMO;
-
     public static final String PROPERTY_OPERATION_ID = "operation." + Operation.PROPERTY_ID;
 
-    public static final String PROPERTY_VOYAGE_NAME = PROPERTY_VOYAGE + "." + Voyage.PROPERTY_NAME;
+    public static final String PROPERTY_VOYAGE_NAME = "voyage." + Voyage.PROPERTY_NAME;
 
-    public static final String PROPERTY_VOYAGE_YEAR = PROPERTY_VOYAGE + "." + Voyage.PROPERTY_START_DATE;
+    public static final String PROPERTY_VOYAGE_YEAR = "voyage." + Voyage.PROPERTY_START_DATE;
 
     public static final String PROPERTY_SEX_CATEGORY = "sexCategory";
 

Modified: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportModel.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportModel.java	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportModel.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -21,27 +21,40 @@
  * #L%
  */
 
+import com.google.common.collect.Lists;
+import fr.ifremer.echobase.csv.EchoBaseCsvUtil;
 import fr.ifremer.echobase.entities.references.Species;
 import org.nuiton.csv.ext.AbstractExportModel;
 
+import java.util.List;
+
 /**
  * Created on 3/5/14.
  *
  * @author Tony Chemit <chemit@codelutin.com>
- * @since XXX
+ * @since 2.6
  */
-public class SpeciesExportModel extends AbstractExportModel<Species> {
+public class SpeciesExportModel extends AbstractExportModel<SpeciesExportRow> {
 
     public SpeciesExportModel(char separator) {
         super(separator);
         newColumnForExport("C_Perm", Species.PROPERTY_TAXON_CODE);
         newColumnForExport("NumSys", Species.PROPERTY_TAXON_SYSTEMATIC_ORDER);
         newColumnForExport("NivSys", Species.PROPERTY_TAXON_SYSTEMATIC_LEVEL);
-        newColumnForExport("C_VALIDE", Species.PROPERTY_CODE_MEMO);
+        newColumnForExport("C_VALIDE", EchoBaseCsvUtil.<SpeciesExportRow, Species>newBeanProperty(SpeciesExportRow.PROPERTY_SPECIES), EchoBaseCsvUtil.SPECIES_TO_COSER_CODE);
         newColumnForExport("L_VALIDE", Species.PROPERTY_GENUS_SPECIES);
         newColumnForExport("AA_VALIDE", Species.PROPERTY_AUTHOR_REFERENCE);
         newColumnForExport("C_TxPère", Species.PROPERTY_TAXON_FATHER_MEMOCODE);
         newColumnForExport("Taxa", "taxaCode");
     }
 
+    public List<SpeciesExportRow> toRows(List<Species> speciesList) {
+        List<SpeciesExportRow> rows = Lists.newArrayList();
+        for (Species species : speciesList) {
+            SpeciesExportRow row = new SpeciesExportRow();
+            row.setSpecies(species);
+            rows.add(row);
+        }
+        return rows;
+    }
 }

Added: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java
===================================================================
--- trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java	                        (rev 0)
+++ trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java	2014-04-05 16:58:54 UTC (rev 1005)
@@ -0,0 +1,52 @@
+package fr.ifremer.echobase.services.service.exportCoser;
+
+import fr.ifremer.echobase.entities.references.Species;
+
+/**
+ * Created on 4/5/14.
+ *
+ * @author Tony Chemit <chemit@codelutin.com>
+ * @since 2.6
+ */
+public class SpeciesExportRow {
+
+    public static final String PROPERTY_SPECIES = "species";
+
+    protected Species species;
+
+    public Species getSpecies() {
+        return species;
+    }
+
+    public String getTaxaCode() {
+        return "";
+    }
+
+    public String getGenusSpecies() {
+        return species.getGenusSpecies();
+    }
+
+    public String getTaxonCode() {
+        return species.getTaxonCode();
+    }
+
+    public String getTaxonSystematicOrder() {
+        return species.getTaxonSystematicOrder();
+    }
+
+    public String getTaxonSystematicLevel() {
+        return species.getTaxonSystematicLevel();
+    }
+
+    public String getTaxonFatherMemocode() {
+        return species.getTaxonFatherMemocode();
+    }
+
+    public String getAuthorReference() {
+        return species.getAuthorReference();
+    }
+
+    public void setSpecies(Species species) {
+        this.species = species;
+    }
+}


Property changes on: trunk/echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser/SpeciesExportRow.java
___________________________________________________________________
Added: svn:keywords
   + Author Date Id Revision
Added: svn:eol-style
   + native

Modified: trunk/echobase-ui/src/main/resources/struts.xml
===================================================================
--- trunk/echobase-ui/src/main/resources/struts.xml	2014-04-05 13:02:18 UTC (rev 1004)
+++ trunk/echobase-ui/src/main/resources/struts.xml	2014-04-05 16:58:54 UTC (rev 1005)
@@ -124,8 +124,8 @@
         <interceptor-ref name="exception"/>
         <interceptor-ref name="alias"/>
         <interceptor-ref name="servletConfig"/>
+        <interceptor-ref name="i18n"/>
         <interceptor-ref name="echobaseInjector"/>
-        <interceptor-ref name="i18n"/>
         <interceptor-ref name="prepare"/>
         <interceptor-ref name="chain"/>
         <interceptor-ref name="scopedModelDriven"/>

    

r1005 - in trunk: echobase-domain/src/main/java/fr/ifremer/echobase/csv echobase-domain/src/main/java/fr/ifremer/echobase/entities/references echobase-services/src/main/java/fr/ifremer/echobase/services/service/exportCoser echobase-ui/src/main/resources

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